2 muutettua tiedostoa jossa 2 lisäystä ja 2 poistoa
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defaults
Näytä tiedosto
| @@ -17,7 +17,7 @@ | |||
| "interval_padding": "100", | |||
| "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02", | |||
| "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3", | |||
| "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04", | |||
| "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2019.10", | |||
| "tnseq_pon": "", | |||
| "tnscope_pon": "", | |||
| "disk_size": "200", | |||
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tasks/annovar.wdl
Näytä tiedosto
| @@ -14,7 +14,7 @@ task annovar { | |||
| set -o pipefail | |||
| set -e | |||
| nt=$(nproc) | |||
| /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -hgvs -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt | |||
| >>> | |||
| runtime { | |||
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